README.md

# DGL-LifeSci

## Introduction

Deep learning on graphs has been an arising trend in the past few years. There are a lot of graphs in 
life science such as molecular graphs and biological networks, making it an import area for applying 
deep learning on graphs. DGL-LifeSci is a DGL-based package for various applications in life science 
with graph neural networks. 

We provide various functionalities, including but not limited to methods for graph construction, 
featurization, and evaluation, model architectures, training scripts and pre-trained models.

**For a full list of work implemented in DGL-LifeSci, see [here](examples/README.md).**

## Installation

### Requirements

DGL-LifeSci should work on

* all Linux distributions no earlier than Ubuntu 16.04
* macOS X
* Windows 10

DGL-LifeSci requires python 3.6+, DGL 0.4.3+ and PyTorch 1.2.0+.

Additionally, we require `RDKit 2018.09.3` for cheminformatics. We recommend installing it with

```
conda install -c conda-forge rdkit==2018.09.3
```
 
For other installation recipes for RDKit, see the [official documentation](https://www.rdkit.org/docs/Install.html).

### Pip installation for DGL-LifeSci

```
pip install dgllife
```

### Conda installation for DGL-LifeSci

```
conda install -c dglteam dgllife
```

### Installation from source

If you want to try experimental features, you can install from source as follows:

```
git clone https://github.com/dmlc/dgl.git
cd apps/life_sci/python
python setup.py install
```

### Verifying successful installation

Once you have installed the package, you can verify the success of installation with 

```python
import dgllife

print(dgllife.__version__)
# 0.2.1
```

If you are new to DGL, the first time you import dgl a message will pop up as below:

```
DGL does not detect a valid backend option. Which backend would you like to work with?
Backend choice (pytorch, mxnet or tensorflow):
```

and you need to enter `pytorch`.

## Example Usage

To apply graph neural networks to molecules with DGL, we need to first construct `DGLGraph` -- 
the graph data structure in DGL and prepare initial node/edge features. Below gives an example of 
constructing a bi-directed graph from a molecule and featurizing it with atom and bond features such 
as atom type and bond type.

```python
from dgllife.utils import smiles_to_bigraph, CanonicalAtomFeaturizer, CanonicalBondFeaturizer

# Node featurizer
node_featurizer = CanonicalAtomFeaturizer(atom_data_field='h')
# Edge featurizer
edge_featurizer = CanonicalBondFeaturizer(bond_data_field='h')
# SMILES (a string representation for molecule) for Penicillin
smiles = 'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C'
g = smiles_to_bigraph(smiles=smiles, 
                      node_featurizer=node_featurizer,
                      edge_featurizer=edge_featurizer)
print(g)
"""
DGLGraph(num_nodes=23, num_edges=50,
         ndata_schemes={'h': Scheme(shape=(74,), dtype=torch.float32)}
         edata_schemes={'h': Scheme(shape=(12,), dtype=torch.float32)})
"""
```

We implement various models that users can import directly. Below gives an example of defining a GCN-based model  
for molecular property prediction.

```python
from dgllife.model import GCNPredictor

model = GCNPredictor(in_feats=1)
```

For a full example of applying `GCNPredictor`, run the following command

```bash
python examples/property_prediction/classification.py -m GCN -d Tox21
```

For more examples on molecular property prediction, generative models, protein-ligand binding affinity 
prediction and reaction prediction, see `examples`.

We also provide pre-trained models for most examples, which can be used off-shelf without training from scratch. 
Below gives an example of loading a pre-trained model for `GCNPredictor` on a molecular property prediction dataset.

```python
from dgllife.data import Tox21
from dgllife.model import load_pretrained
from dgllife.utils import smiles_to_bigraph, CanonicalAtomFeaturizer

dataset = Tox21(smiles_to_bigraph, CanonicalAtomFeaturizer())
model = load_pretrained('GCN_Tox21') # Pretrained model loaded
model.eval()

smiles, g, label, mask = dataset[0]
feats = g.ndata.pop('h')
label_pred = model(g, feats)
print(smiles)                   # CCOc1ccc2nc(S(N)(=O)=O)sc2c1
print(label_pred[:, mask != 0]) # Mask non-existing labels
# tensor([[ 1.4190, -0.1820,  1.2974,  1.4416,  0.6914,  
# 2.0957,  0.5919,  0.7715, 1.7273,  0.2070]])
```

Similarly, we can load a pre-trained model for generating molecules. If possible, we recommend running 
the code block below with Jupyter notebook.

```python
from dgllife.model import load_pretrained

model = load_pretrained('DGMG_ZINC_canonical')
model.eval()
smiles = []
for i in range(4):
    smiles.append(model(rdkit_mol=True))

print(smiles)
# ['CC1CCC2C(CCC3C2C(NC2=CC(Cl)=CC=C2N)S3(=O)=O)O1',
# 'O=C1SC2N=CN=C(NC(SC3=CC=CC=N3)C1=CC=CO)C=2C1=CCCC1', 
# 'CC1C=CC(=CC=1)C(=O)NN=C(C)C1=CC=CC2=CC=CC=C21', 
# 'CCN(CC1=CC=CC=C1F)CC1CCCN(C)C1']
```

If you are running the code block above in Jupyter notebook, you can also visualize the molecules generated with

```python
from IPython.display import SVG
from rdkit import Chem
from rdkit.Chem import Draw

mols = [Chem.MolFromSmiles(s) for s in smiles]
SVG(Draw.MolsToGridImage(mols, molsPerRow=4, subImgSize=(180, 150), useSVG=True))
```

![](https://data.dgl.ai/dgllife/dgmg/dgmg_model_zoo_example2.png)

## Speed Reference

Below we provide some reference numbers to show how DGL improves the speed of training models per epoch in seconds.

| Model                              | Original Implementation | DGL Implementation | Improvement |
| ---------------------------------- | ----------------------- | ------------------ | ----------- |
| GCN on Tox21                       | 5.5 (DeepChem)          | 1.0                | 5.5x        |
| AttentiveFP on Aromaticity         | 6.0                     | 1.2                | 5x          |
| JTNN on ZINC                       | 1826                    | 743                | 2.5x        |
| WLN for reaction center prediction | 11657                   | 5095               | 2.3x        |                                                           |